Welcome to the PREX database

Peroxiredoxin proteins1 (EC are a family of thioredoxin-scaffold enzymes with cysteine-dependent peroxidase activity on hydrogen peroxide and larger hydroperoxide substrates.

PREX2 is a database of peroxiredoxin (Prx or PRDX) protein ids and sequences unambiguously classified into one of six distinct subclasses based on the Deacon Active Site Profiler (DASP) bioinformatics tool3 using structural information around active sites to focus in on function-relevant sequence information. The signatures from Prx proteins of known structure were then used to generate a subclass-specific profile for searching GenBank Genbank(nr), Nov 2010 edition4.

Prx subclassification, which is difficult or impossible given only scant or misleading nomenclature in the Prx literature, is important for highlighting differences or similarities between Prx members in:

Searches of this database can be conducted by protein name or ID, organism name or sequence for those previously identified by us (Genbank(nr), Nov 2010 edition), or by BLAST search of any query sequence to find the closest relatives among the previously subclassified Prxs.

Output includes the subfamily to which the query sequence belongs (or the subfamily assignments for the similar proteins identified in the BLAST output), accession and gi numbers, genus and species, the p-value for the search, and the active site signature generated by DASP. Information for the relevant subfamily can then be accessed through a link, giving a synopsis of the characteristics of members of that family, some pertinent references, and a multiple sequence alignment (MSA) of 4-5 selected members of this subfamily and one representative from each of the other subfamilies.

Subfamilies identified are denoted by the name of a canonical (usually founding) member:

For more information, go to:


  1. Wood, Z.A., Schröder E., Harris J.R., and Poole L.B. (2003). Structure, mechanism and regulation of peroxiredoxins. Trends Biochem Sci, 28, 32-40. PMID: 12517450
  2. Soito L., Williamson C., Knutson S.T., Fetrow J.S., Poole L.B., and Nelson K.J. (2011). PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. Nucleic Acids Res., 39(Database issue):D332-337. PMID: 21036863
  3. Fetrow, J.S. (2006). Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP). In Curr Protoc in Bioinformatics. (pp. 8.10.1–8.10.16). New York: Wiley. PMID: 18428769
  4. Nelson, K. J., Knutson, S. T., Soito L., Klomsiri C., Poole, L. B., and Fetrow, J. S. (2011). Analysis of the peroxiredoxin family: using active site structure and sequence information for global classification and residue analysis. Proteins, 79, 947-964. PMID: 21181731